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Detailed information for vg1006743994:

Variant ID: vg1006743994 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 6743994
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGAGGCATCACAAAATGGTGTTTTTATTTTTTTTTTTGAGAATTACACAGTACAACGCAGACACTCACAATGCACGCGCACTCACCCCTATGAACACACG[C/T]
ACGCAAACCCTACCCCTATGAGCATCTTCGAAGACTGGGCCGGTAAATCCTGGAGAGATTGACGAAGTCACCACAGGCGCCTCGCTGTCGACGGGTACGT

Reverse complement sequence

ACGTACCCGTCGACAGCGAGGCGCCTGTGGTGACTTCGTCAATCTCTCCAGGATTTACCGGCCCAGTCTTCGAAGATGCTCATAGGGGTAGGGTTTGCGT[G/A]
CGTGTGTTCATAGGGGTGAGTGCGCGTGCATTGTGAGTGTCTGCGTTGTACTGTGTAATTCTCAAAAAAAAAAATAAAAACACCATTTTGTGATGCCTCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.80%	4.80%	8.13%	32.27%	NA
All Indica	2759	57.30%	0.30%	8.63%	33.85%	NA
All Japonica	1512	56.40%	10.60%	7.28%	25.73%	NA
Aus	269	24.90%	0.40%	10.41%	64.31%	NA
Indica I	595	92.80%	0.00%	1.18%	6.05%	NA
Indica II	465	37.80%	0.00%	6.02%	56.13%	NA
Indica III	913	45.30%	0.20%	16.54%	37.90%	NA
Indica Intermediate	786	55.70%	0.60%	6.62%	37.02%	NA
Temperate Japonica	767	77.30%	0.30%	3.39%	19.04%	NA
Tropical Japonica	504	21.00%	28.60%	13.49%	36.90%	NA
Japonica Intermediate	241	63.90%	5.80%	6.64%	23.65%	NA
VI/Aromatic	96	45.80%	50.00%	0.00%	4.17%	NA
Intermediate	90	51.10%	12.20%	8.89%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1006743994	C -> T	LOC_Os10g12130.1	upstream_gene_variant ; 3896.0bp to feature; MODIFIER	silent_mutation	Average:67.141; most accessible tissue: Zhenshan97 panicle, score: 89.846	N	N	N	N
vg1006743994	C -> T	LOC_Os10g12130-LOC_Os10g12140	intergenic_region ; MODIFIER	silent_mutation	Average:67.141; most accessible tissue: Zhenshan97 panicle, score: 89.846	N	N	N	N
vg1006743994	C -> DEL	N	N	silent_mutation	Average:67.141; most accessible tissue: Zhenshan97 panicle, score: 89.846	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1006743994	2.24E-06	NA	mr1136	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	7.53E-08	mr1136	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	2.56E-11	mr1570	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	7.45E-07	mr1642	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	2.99E-07	mr1057_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	3.88E-07	mr1195_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	1.69E-06	1.69E-06	mr1333_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	3.81E-07	mr1438_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	8.48E-06	NA	mr1480_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	4.69E-06	NA	mr1482_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	1.24E-06	NA	mr1482_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	1.97E-07	mr1653_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	1.31E-06	mr1705_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	NA	9.80E-06	mr1735_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1006743994	6.50E-06	NA	mr1800_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251